Locus 6373

Sequence ID	X_DroMel_CAF1
Location	16,020,874 – 16,021,010
Length	136
Max. P	0.968031

overview

Window 1

Location	16,020,874 – 16,020,970
Length	96
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.83
Mean single sequence MFE	-35.64
Consensus MFE	-31.02
Energy contribution	-30.98
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.87
SVM decision value	0.78
SVM RNA-class probability	0.848904
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16020874 96 + 22224390
UGACGGCACGGGGAUGGUGGCAUGAUG-----------------------GUCAGUUCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGAA
....((((.((((((((.((((((..(-----------------------((..(((((((-..(....)..))))))).....)))..)))))).)).....)))))).))))...... ( -33.90)
>DroSec_CAF1 88593 96 + 1
UGACGGCACGGGGAUGGUGGCACGAUG-----------------------GUCAGUUCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGA
....((((.((((((((.((((((..(-----------------------((..(((((((-..(....)..))))))).....)))..)))))).)).....)))))).))))...... ( -35.70)
>DroSim_CAF1 82625 96 + 1
UGACGGCACGGGGAUGGUGGCACGAUG-----------------------GUCAGUUCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGA
....((((.((((((((.((((((..(-----------------------((..(((((((-..(....)..))))))).....)))..)))))).)).....)))))).))))...... ( -35.70)
>DroEre_CAF1 86614 96 + 1
UGACGGCACGGGGAUGGUGGCAUGAUG-----------------------GUAAGUGCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGA
....((((.((((((((.((((((..(-----------------------((...((((((-..(....)..)))..)))....)))..)))))).)).....)))))).))))...... ( -30.10)
>DroYak_CAF1 72093 120 + 1
UGACGGCACGGGGAUGGUGGCAUGGUGGCAUGGUGGCACGAUGGUCAGUGGUCAGUUCGGCGAGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGA
....((((.(((((..((((((((....))))(.((((((.((..(...)..))(((((((...(....)..)))))))..........)))))).)))).)..))))).))))...... ( -42.80)
>consensus
UGACGGCACGGGGAUGGUGGCAUGAUG_______________________GUCAGUUCGGC_AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGA
....((((.((((((((.((((((..............................(((((((...(....)..)))))))((.....)).)))))).)).....)))))).))))...... (-31.02 = -30.98 +  -0.04)

alignment

secondary structure

dotplot

Window 2

Location	16,020,901 – 16,021,010
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.36
Mean single sequence MFE	-38.58
Consensus MFE	-34.44
Energy contribution	-34.12
Covariance contribution	-0.32
Combinations/Pair	1.06
Mean z-score	-1.64
Structure conservation index	0.89
SVM decision value	1.62
SVM RNA-class probability	0.968031
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16020901 109 + 22224390
----------GUCAGUUCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGAAUGUCCGAGGAUGUGCGGCGAAGUCCGAGGAUAUUUGACCA
----------(((.....(((-((((((((((((.(((......((....))....))))))))))))))))))...((((((((..((((..........))))..))))))))))).. ( -38.60)
>DroSec_CAF1 88620 109 + 1
----------GUCAGUUCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGAUGUCCGAGGAUGUGCGGCGAAGUCCGAGGAUAUUUGACCA
----------((((....(((-((((((((((((.(((......((....))....))))))))))))))))))....(((((((..((((..........))))..))))))))))).. ( -38.20)
>DroSim_CAF1 82652 109 + 1
----------GUCAGUUCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGAUGUCCGAGGAUGUGCGGCGAAGUCCGAGGAUAUUUGACCA
----------((((....(((-((((((((((((.(((......((....))....))))))))))))))))))....(((((((..((((..........))))..))))))))))).. ( -38.20)
>DroEre_CAF1 86641 109 + 1
----------GUAAGUGCGGC-AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGAUGUCCGAGGAUGUGCGGCGAAGUCCGAGGAUAUUUGGCCG
----------........(((-((((((((((((.(((......((....))....)))))))))))))))))).(..(((((((..((((..........))))..)))))))..)... ( -38.00)
>DroYak_CAF1 72133 120 + 1
AUGGUCAGUGGUCAGUUCGGCGAGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGAUGUCCGAGGAUGUGCGGCGAAGUCCGAGGAUAUUUGACCA
.(((((((..(((...(((((((((((.((((((..........))))..)).)))))).((((((.(..((((.((((....)))).)))).).))))))).)))).)))..))))))) ( -39.90)
>consensus
__________GUCAGUUCGGC_AGGGGGACAAGUCGAGCAAAUAACUUACGUGCCUCUCAUUUGUCUCUUUGUCAUUGGAUGUCCGAGGAUGUGCGGCGAAGUCCGAGGAUAUUUGACCA
..................(((.((((((((((((.(((......((....))....)))))))))))))))))).(..(((((((..((((..........))))..)))))))..)... (-34.44 = -34.12 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:03 2006